3fpl

Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH
(see also Tetrameric alcohol dehydrogenases)



The NADP+-dependent alcohol dehydrogenases (EC 1.1.1.2) from the thermophile Thermoanaerobacter brockii (TbADH), the mesophilic bacterium Clostridium beijerinckii (CbADH), and the protozoan parasite Entamoeba histolytica (EhADH1) are homotetrameric (monomers are colored in different colors) secondary alcohol dehydrogenases. Each monomer of these alcohol dehydrogenases consists of two domains: the cofactor-binding domain  (residues 154−294 for TbADH) and the catalytic domain (residues 1−153 and 295−351 for TbADH ; contains Zn2+ at the active site) separated by a deep cleft. Although, all these three ADHs revealed a high degree of sequence conservation (62-75% identity), them significantly differ in thermostability. The cofactor-binding domains (residues 153−295) of TbADH, CbADH, and EhADH1 were mutually exchanged and 3 corresponding chimeras were constructed. The cofactor-binding domain of thermophilic TbADH was replaced with the cofactor-binding domain of its mesophilic counterpart CbADH (chimera Χ21(TCT), 3fsr). This domain replacement significantly destabilized the parent thermophilic enzyme (ΔT1/2 = −18 °C). But the reverse exchange in CbADH (chimera Χ22(CTC), 3fpl), had little effect on the thermal stability of the parent mesophilic protein. The exchange of the cofactor-binding domain of TbADH with the homologous domain of EhADH1 (chimera Χ23(TET), 3fpc) substantially reduced the thermal stability of the thermophilic ADH (ΔT1/2 = −51 °C) and interfered the oligomerization of the enzyme.

The double mutant of the chimera Χ21(TCT) (cofactor-binding domain of thermophilic TbADH replaced by that of mesophilic CbADH) Q165E/S254K-X21(TCT) (3ftn) was constructed by site-directed mutagenesis. In both TbADH and CbADH, Lys257 and Asp237 form an intrasubunit ion pair, in TbADH, Asp237 is also involved in an ion pair bridge with Arg304 of the adjacent monomer. In addition, Arg304 forms intersubunit salt bridge with Glu165 of the first monomer. Therefore, a four-member ion pair network involving Lys257, Asp237, and Glu165 of one monomer and Arg304 of the adjacent one is present in TbADH (the names of monomers are in brackets). However in mesophilic CbADH (and, therefore, in the chimera Χ21(TCT), 3fsr) the Gln is situated in position 165 (instead Glu of TbADH) and Met in position 304 (instead Arg of TbADH), so, such an ion pair network does not exist. In the double mutant Q165E/S254K-X21(TCT) reverse mutation Q165E reconstructs this network (as in parent thermophilic TbADH) that led to significant enhancement of the thermal stability of CbADH (ΔT1/260 min = 5.4 °C). Chimera X21(TCT) (3fsr) is colored magenta and the double mutant Q165E/S254K-X21(TCT) cyan (3ftn). In chimera X21(TCT), position 254 is occupied by Ser (due to sequence of exchanged domain). The replacement of Ser254 of CbADH with Lys significantly enhances the stability of the enzyme, due to the formation of intrasubunit Lys254 and Glu280 ion pair. However, this replacing of Ser254 by Lys had a negligible effect on the thermal stability, in contrast to mutation Q165E mentioned above.

The comparison of overall Cα backbone of all these chimeras (rmsd 0.45-0.65 Å) with those of the parent enzymes, did not reveal significant structural changes. So, the differences in the thermal stability of the chimeras and the parent enzymes could be caused by relatively small specific changes located at the important points of the NADP+-dependent alcohol dehydrogenases. For example see Cα superposition for the X23(TET) chimera (red) (3fpc) and its parent ADHs (TbADH, colored blue (1ped), and EhADH1, colored lime (1y9a). The RMSDs of the TbADH−EhADH1, TbADH−Χ23(TET), and EhADH1−Χ23(TET) were 0.68, 0.56, and 0.48 Å, respectively.

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About this Structure
3FPL is a 1 chain structure with sequence from Clostridium beijerinckii, thermoanaerobacter brockii. Full crystallographic information is available from OCA.

Reference
Biochemical and structural properties of chimeras constructed by exchange of cofactor binding domains in alcohol dehydrogenases from thermophilic and mesophilic microorganisms., Goihberg E, Peretz M, Tel-Or S, Dym O, Shimon LJ, Frolow F, Burstein Y.Biochemistry. 2010 Jan 26. Epub ahead of print

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